To enable Qt5 applications to be built using the CMake ADT plugin the variable OE_QMAKE_PATH_EXTERNAL_HOST_BINS should be set to $ENV{OECORE_NATIVE_SYSROOT}/usr/bin/qt5 in the generated toolchain.cmake file. This allows the default Qt5 CMake files to correctly configure the build.
Unless I'm misunderstanding, this is something to be dealt with in the meta-qt5 layer which is maintained by the community. If that is true then the openembedded-devel mailing list would be the best place to discuss this and/or send patches. On the other hand if I've got the wrong end of the stick and this is something within the Eclipse plugin itself then please reopen.